Since 1991, the Archaeological Museum of Rethymnon has been housed in the pentagonal building opposite the main gate of the Fortezza. The building was constructed by the Turks in an effort to strengthen the city's defense. Due to the different functions that it served over the centuries - until the 1960's it housed the civic prison - its original form has been significantly altered.

The museum contains the following collections:

Late Neolithic (3500-2900 B.C.) and Early Minoan (2800-2100 B.C.) finds from the caves Gerani, Melidoni, Margeles and Helenes

finds from the buildings at Apodoulou, Monastiraki and the peak sanctuary at Vrysinas, dated to the Middle Minoan period (2100-1600 B.C.)

Late Minoan finds (1600-1100 B.C.) from the cemeteries, the most representative being that of Armenoi

finds of the Geometric (1000-700 B.C.) and Archaic (700-500 B.C.) periods from Eleutherna and Axos

finds from Stavromenos and Argyroupolis (ancient Lappa) dated to the Classical, Hellenistic and Roman periods.

The most important items of the exhibition are:Clay larnaxdecorated with a hunting scene. Found at the Late Minoan cemetery of Armenoi (1320-1200 B.C.).

Figurine of the Minoan goddess. The statuette represents the well-known Minoan female deity with upraised hands. It was found at Pangalochori and dates from the Late Minoan period (1320-1200 B.C.).

Marble statue of Aphrodite. Roman copy of a Greek original, found at Argyroupolis. Dated to the 1st century A.D.

Marble violin-shaped figurine. It was found in the Gerani cave and dates from the Late Neolithic period (3600-3200 B.C.).

Clay model of a shrine. Preserved only in the upper part, it represents the upper floor of the shrine. It was found at Monasteraki and dates from the Middle Minoan period (1800-1700 B.C.).

Stone model of an offering table. The fragment preserves part of a Linear A inscription. It was found at the peak sanctuary of Vrysinas and dates from the Middle Minoan period (1700-1600 B.C.).

Pyxis strainer from Stavromenos. Clay footed vase with a lid and perforated base. The surface is decorated with painted rows of spirals and floral patterns. Dated to the Late Minoan period (1500-1450 B.C.).

Head of a terracotta female figurine. Found at Axos and dated to 530 B.C.

Part of a marble funerary stele. It bears the relief representation of a warrior carrying a shield. It was found at Eleutherna and is dated to the second half of the 6th century B.C.

Part of a marble funerary stele. A standing naked athlete is depicted, accompanied by his dog. It was found at Stavromenos and dates from around 460 B.C.